/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.appletgui;
import java.awt.*;
+import java.awt.event.*;
+
+import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
AlignViewport av;
String[] renderOrder;
FontMetrics fm;
+
int charOffset;
float transparency = 1f;
/**
* Creates a new FeatureRenderer object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
*/
public FeatureRenderer(AlignViewport av)
{
featureGroups = fr.featureGroups;
featureColours = fr.featureColours;
transparency = fr.transparency;
+ if (av!=null && fr.av!=null && fr.av!=av)
+ {
+ if (fr.av.featuresDisplayed!=null)
+ {
+ if (av.featuresDisplayed==null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ } else {
+ av.featuresDisplayed.clear();
+ }
+ Enumeration en=fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+ }
+ }
}
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+ static String lastFeatureAdded;
+
+ static String lastFeatureGroupAdded;
+
+ static String lastDescriptionAdded;
+
+ int featureIndex = 0;
+
+ boolean deleteFeature = false;
+
+ FeatureColourPanel colourPanel;
+
+ class FeatureColourPanel extends Panel
{
- overview = true;
- if (!av.showSequenceFeatures)
+ String label = "";
+
+ private Color maxCol;
+
+ private boolean isColourByLabel, isGcol;
+
+ /**
+ * render a feature style in the amend feature dialog box
+ */
+ public void updateColor(Object newcol)
{
- return initialCol;
+
+ Color bg, col = null;
+ GraduatedColor gcol = null;
+ String vlabel = "";
+ if (newcol instanceof Color)
+ {
+ isGcol = false;
+ col = (Color) newcol;
+ gcol = null;
+ }
+ else if (newcol instanceof GraduatedColor)
+ {
+ isGcol = true;
+ gcol = (GraduatedColor) newcol;
+ col = null;
+ }
+ else
+ {
+ throw new Error("Invalid color for MyCheckBox");
+ }
+ if (col != null)
+ {
+ setBackground(bg = col);
+ }
+ else
+ {
+ if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "
+ + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
+ : "(<)");
+ }
+ if (isColourByLabel = gcol.isColourByLabel())
+ {
+ setBackground(bg = Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(bg = gcol.getMinColor());
+ maxCol = gcol.getMaxColor();
+ }
+ }
+ label = vlabel;
+ setBackground(bg);
+ repaint();
}
- lastSequence = seq;
- sequenceFeatures = lastSequence.getSequenceFeatures();
- if (sequenceFeatures == null)
+ FeatureColourPanel()
{
- return initialCol;
+ super(null);
}
- sfSize = sequenceFeatures.length;
+ public void paint(Graphics g)
+ {
+ Dimension d = getSize();
+ if (isGcol)
+ {
+ if (isColourByLabel)
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ g.setColor(Color.black);
+ Font f = new Font("Verdana", Font.PLAIN, 10);
+ g.setFont(f);
+ g.drawString("Label", 0, 0);
+ }
+ else
+ {
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+ }
+ }
+ }
+
+ }
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
+ {
+ Panel bigPanel = new Panel(new BorderLayout());
+ final TextField name = new TextField(16);
+ final TextField source = new TextField(16);
+ final TextArea description = new TextArea(3, 35);
+ final TextField start = new TextField(8);
+ final TextField end = new TextField(8);
+ final Choice overlaps;
+ Button deleteButton = new Button("Delete");
+ deleteFeature = false;
+
+ colourPanel = new FeatureColourPanel();
+ colourPanel.setSize(110, 15);
+ final FeatureRenderer fr = this;
+
+ Panel panel = new Panel(new GridLayout(3, 1));
+
+ featureIndex = 0; // feature to be amended.
+ Panel tmp;
+
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
{
- return Color.white;
+ panel = new Panel(new GridLayout(4, 1));
+ tmp = new Panel();
+ tmp.add(new Label("Select Feature: "));
+ overlaps = new Choice();
+ for (int i = 0; i < features.length; i++)
+ {
+ String item = features[i].getType() + "/" + features[i].getBegin()
+ + "-" + features[i].getEnd();
+
+ if (features[i].getFeatureGroup() != null)
+ item += " (" + features[i].getFeatureGroup() + ")";
+
+ overlaps.addItem(item);
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new java.awt.event.ItemListener()
+ {
+ public void itemStateChanged(java.awt.event.ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ name.setText(features[index].getType());
+ description.setText(features[index].getDescription());
+ source.setText(features[index].getFeatureGroup());
+ start.setText(features[index].getBegin() + "");
+ end.setText(features[index].getEnd() + "");
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ Object col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+
+ colourPanel.updateColor(col);
+ }
+ });
+
+ panel.add(tmp);
}
+ // ////////
+ // ////////////////////////////////////
- currentColour = null;
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(name);
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Group: ", Label.RIGHT));
+ tmp.add(source);
- if (currentColour == null)
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(colourPanel);
+
+ bigPanel.add(panel, BorderLayout.NORTH);
+
+ panel = new Panel();
+ panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new ScrollPane().add(description));
+
+ if (!newFeatures)
{
- return initialCol;
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new Panel();
+ panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(start);
+ panel.add(new Label(" End:", Label.RIGHT));
+ panel.add(end);
+ bigPanel.add(panel, BorderLayout.CENTER);
+ }
+ else
+ {
+ bigPanel.add(panel, BorderLayout.CENTER);
}
- return new Color( ( (Integer) currentColour).intValue());
- }
+ if (lastFeatureAdded == null)
+ {
+ if (features[0].type != null)
+ {
+ lastFeatureAdded = features[0].type;
+ }
+ else
+ {
+ lastFeatureAdded = "feature_1";
+ }
+ }
- /**
- * This is used by the Molecule Viewer to get the accurate colour
- * of the rendered sequence
- */
- boolean overview = false;
+ if (lastFeatureGroupAdded == null)
+ {
+ if (features[0].featureGroup != null)
+ {
+ lastFeatureGroupAdded = features[0].featureGroup;
+ }
+ else
+ {
+ lastFeatureAdded = "Jalview";
+ }
+ }
- int white = Color.white.getRGB();
- public int findFeatureColour(int initialCol, int seqIndex, int column)
- {
- if (!av.showSequenceFeatures)
+ String title = newFeatures ? "Create New Sequence Feature(s)"
+ : "Amend/Delete Features for " + sequences[0].getName();
+
+ final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+ 240);
+
+ dialog.setMainPanel(bigPanel);
+
+ if (newFeatures)
{
- return initialCol;
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
+ }
+ else
+ {
+ dialog.ok.setLabel("Amend");
+ dialog.buttonPanel.add(deleteButton, 1);
+ deleteButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ deleteFeature = true;
+ dialog.setVisible(false);
+ }
+ });
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
+ }
+
+ start.setText(features[0].getBegin() + "");
+ end.setText(features[0].getEnd() + "");
+ description.setText(features[0].getDescription());
+ Color col = getColour(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+ Object fcol = getFeatureStyle(name.getText());
+ // simply display the feature color in a box
+ colourPanel.updateColor(fcol);
+ dialog.setResizable(true);
+ // TODO: render the graduated color in the box.
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ {
+ public void mousePressed(java.awt.event.MouseEvent evt)
+ {
+ if (!colourPanel.isGcol)
+ {
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ else
+ {
+ FeatureColourChooser fcc = new FeatureColourChooser(
+ ap.alignFrame, name.getText());
+ dialog.transferFocus();
+ }
+ }
+ });
+ dialog.setVisible(true);
+
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+ if (dialog.accept)
+ {
+ // This ensures that the last sequence
+ // is refreshed and new features are rendered
+ lastSeq = null;
+ lastFeatureAdded = name.getText().trim();
+ lastFeatureGroupAdded = source.getText().trim();
+ lastDescriptionAdded = description.getText().replace('\n', ' ');
}
- if (seqIndex != lastSequenceIndex)
+ if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+ lastFeatureGroupAdded = null;
+
+ if (!newFeatures)
{
- lastSequence = av.alignment.getSequenceAt(seqIndex);
- lastSequenceIndex = seqIndex;
- sequenceFeatures = lastSequence.getSequenceFeatures();
- if (sequenceFeatures == null)
+
+ SequenceFeature sf = features[featureIndex];
+ if (dialog.accept)
{
- return initialCol;
+ sf.type = lastFeatureAdded;
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ if (!colourPanel.isGcol)
+ {
+ // update colour - otherwise its already done.
+ setColour(sf.type, colourPanel.getBackground());
+ }
+ try
+ {
+ sf.begin = Integer.parseInt(start.getText());
+ sf.end = Integer.parseInt(end.getText());
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ ffile.parseDescriptionHTML(sf, false);
+ }
+ if (deleteFeature)
+ {
+ sequences[0].deleteFeature(sf);
}
- sfSize = sequenceFeatures.length;
+ }
+ else
+ {
+ if (dialog.accept && name.getText().length() > 0)
+ {
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features[i].type = lastFeatureAdded;
+ features[i].featureGroup = lastFeatureGroupAdded;
+ features[i].description = lastDescriptionAdded;
+ sequences[i].addSequenceFeature(features[i]);
+ ffile.parseDescriptionHTML(features[i], false);
+ }
+
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+
+ if (featureGroups == null)
+ {
+ featureGroups = new Hashtable();
+ }
+
+ col = colourPanel.getBackground();
+ // setColour(lastFeatureAdded, fcol);
+
+ if (lastFeatureGroupAdded != null)
+ {
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+ }
+ if (fcol instanceof Color)
+ {
+ setColour(lastFeatureAdded, fcol);
+ }
+ av.featuresDisplayed.put(lastFeatureAdded,
+ getFeatureStyle(lastFeatureAdded));
+
+ findAllFeatures();
+
+ String[] tro = new String[renderOrder.length];
+ tro[0] = renderOrder[renderOrder.length - 1];
+ System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1);
+ renderOrder = tro;
+ }
+ else
+ {
+ // no update to the alignment
+ return false;
+ }
+ }
+ // refresh the alignment and the feature settings dialog
+ if (av.featureSettings != null)
+ {
+ av.featureSettings.refreshTable();
+ }
+ // findAllFeatures();
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+ {
+ overview = true;
+ if (!av.showSequenceFeatures)
+ {
+ return initialCol;
}
- if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+ lastSeq = seq;
+ sequenceFeatures = lastSeq.getSequenceFeatures();
+ if (sequenceFeatures == null)
{
- return Color.white.getRGB();
+ return initialCol;
+ }
+
+ sfSize = sequenceFeatures.length;
+
+ if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))
+ {
+ return Color.white;
}
currentColour = null;
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
+ drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);
if (currentColour == null)
{
return initialCol;
}
- return ( (Integer) currentColour).intValue();
+ return new Color(((Integer) currentColour).intValue());
}
/**
+ * This is used by the Molecule Viewer to get the accurate colour of the
+ * rendered sequence
+ */
+ boolean overview = false;
+
+ /**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param seq DOCUMENT ME!
- * @param sg DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ * @param sg
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ * @param x1
+ * DOCUMENT ME!
+ * @param y1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
// String type;
// SequenceFeature sf;
- int lastSequenceIndex = -1;
- SequenceI lastSequence;
+ SequenceI lastSeq;
+
SequenceFeature[] sequenceFeatures;
+
int sfSize, sfindex, spos, epos;
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
+ synchronized public void drawSequence(Graphics g, SequenceI seq,
+ int start, int end, int y1)
{
if (seq.getSequenceFeatures() == null
- || seq.getSequenceFeatures().length == 0)
+ || seq.getSequenceFeatures().length == 0)
{
return;
}
{
transparencySetter.setTransparency(g, transparency);
}
-
- if (lastSequence == null || seq != lastSequence || sequenceFeatures!=seq.getSequenceFeatures())
+
+ if (lastSeq == null || seq != lastSeq
+ || sequenceFeatures != seq.getSequenceFeatures())
{
- lastSequence = seq;
+ lastSeq = seq;
sequenceFeatures = seq.getSequenceFeatures();
sfSize = sequenceFeatures.length;
}
}
if (!overview)
{
- spos = lastSequence.findPosition(start);
- epos = lastSequence.findPosition(end);
+ spos = lastSeq.findPosition(start);
+ epos = lastSeq.findPosition(end);
if (g != null)
{
fm = g.getFontMetrics();
}
if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
+ && sequenceFeatures[sfindex].featureGroup != null
+ && featureGroups
+ .containsKey(sequenceFeatures[sfindex].featureGroup)
+ && !((Boolean) featureGroups
+ .get(sequenceFeatures[sfindex].featureGroup))
+ .booleanValue())
{
continue;
}
- if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
+ if (!overview
+ && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+ .getEnd() < spos))
{
continue;
}
if (overview)
{
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
+ if (sequenceFeatures[sfindex].begin <= start
+ && sequenceFeatures[sfindex].end >= start)
{
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
+ currentColour = new Integer(
+ getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type);
}
}
{
renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ getColour(sequenceFeatures[sfindex])
+ // new Color(((Integer) av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type)).intValue())
+ , start, end, y1);
renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex])
+ // new Color(((Integer) av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type)).intValue())
+ , start, end, y1);
}
else
{
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
+ if (showFeature(sequenceFeatures[sfindex]))
+ {
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1);
+ }
}
}
}
char s;
+
int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
+
+ void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
+ Color featureColour, int start, int end, int y1)
{
- if ( ( (fstart <= end) && (fend >= start)))
+ if (((fstart <= end) && (fend >= start)))
{
if (fstart < start)
{ // fix for if the feature we have starts before the sequence start,
g.setColor(featureColour);
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+ g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
+ av.charHeight);
if (!av.validCharWidth)
{
g.setColor(Color.white);
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+ g.drawString(String.valueOf(s), charOffset
+ + (av.charWidth * (i - start)), (y1 + av.charHeight)
+ - av.charHeight / 5); // pady = height / 5;
}
}
}
+ Hashtable minmax = null;
+
+ /**
+ * Called when alignment in associated view has new/modified features to
+ * discover and display.
+ *
+ */
+ public void featuresAdded()
+ {
+ lastSeq = null;
+ findAllFeatures();
+ }
+
+ /**
+ * find all features on the alignment
+ */
void findAllFeatures()
{
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
-
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
+ minmax = new Hashtable();
+
for (int i = 0; i < av.alignment.getHeight(); i++)
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i).
- getSequenceFeatures();
+ SequenceFeature[] features = av.alignment.getSequenceAt(i)
+ .getSequenceFeatures();
if (features == null)
{
int index = 0;
while (index < features.length)
{
+ if (features[index].begin == 0 && features[index].end == 0)
+ {
+ index++;
+ continue;
+ }
if (!av.featuresDisplayed.containsKey(features[index].getType()))
{
if (getColour(features[index].getType()) == null)
{
featureColours.put(features[index].getType(),
- ucs.createColourFromName(features[index].
- getType()));
+ ucs.createColourFromName(features[index].getType()));
}
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
+ av.featuresDisplayed.put(features[index].getType(), new Integer(
+ getColour(features[index].getType()).getRGB()));
allfeatures.addElement(features[index].getType());
}
+ if (features[index].score != Float.NaN)
+ {
+ int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
+ float[][] mm = (float[][]) minmax.get(features[index].getType());
+ if (mm == null)
+ {
+ mm = new float[][]
+ { null, null };
+ minmax.put(features[index].getType(), mm);
+ }
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
+ }
+ else
+ {
+ if (mm[nonpos][0] > features[index].score)
+ {
+ mm[nonpos][0] = features[index].score;
+ }
+ if (mm[nonpos][1] < features[index].score)
+ {
+ mm[nonpos][1] = features[index].score;
+ }
+ }
+ }
+
index++;
}
}
}
}
- public Color getColour(String featureType)
+ /**
+ * get a feature style object for the given type string. Creates a
+ * java.awt.Color for a featureType with no existing colourscheme. TODO:
+ * replace return type with object implementing standard abstract colour/style
+ * interface
+ *
+ * @param featureType
+ * @return java.awt.Color or GraduatedColor
+ */
+ public Object getFeatureStyle(String featureType)
{
- return (Color) featureColours.get(featureType);
+ Object fc = featureColours.get(featureType);
+ if (fc == null)
+ {
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+ Color col = ucs.createColourFromName(featureType);
+ featureColours.put(featureType, fc = col);
+ }
+ return fc;
}
- public void addNewFeature(String name, Color col)
+ public Color getColour(String featureType)
{
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + featureType);
+ }
- setColour(name, col);
- if (av.featuresDisplayed == null)
+ /**
+ *
+ * @param sequenceFeature
+ * @return true if feature is visible.
+ */
+ private boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
{
- av.featuresDisplayed = new Hashtable();
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
}
+ else
+ {
+ return true;
+ }
+ }
- av.featuresDisplayed.put(name, "NOGROUP");
+ /**
+ * implement graduated colouring for features with scores
+ *
+ * @param feature
+ * @return render colour for the given feature
+ */
+ public Color getColour(SequenceFeature feature)
+ {
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).findColor(feature);
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + feature.getType());
}
- public void setColour(String featureType, Color col)
+ public void setColour(String featureType, Object col)
{
- featureColours.put(featureType, col);
+ // overwrite
+ // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
+ // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
+ // Object c = featureColours.get(featureType);
+ // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
+ // !((GraduatedColor)c).getMaxColor().equals(_col)))
+ {
+ featureColours.put(featureType, col);
+ }
}
public void setFeaturePriority(Object[][] data)
av.featuresDisplayed.clear();
}
+ /*
+ * if (visibleNew) { if (av.featuresDisplayed != null) {
+ * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new
+ * Hashtable(); } } if (data == null) { return; }
+ */
+
renderOrder = new String[data.length];
if (data.length > 0)
for (int i = 0; i < data.length; i++)
{
String type = data[i][0].toString();
- setColour(type, (Color) data[i][1]);
- if ( ( (Boolean) data[i][2]).booleanValue())
+ setColour(type, data[i][1]);
+ if (((Boolean) data[i][2]).booleanValue())
{
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+ av.featuresDisplayed.put(type, new Integer(getColour(type)
+ .getRGB()));
}
renderOrder[data.length - i - 1] = type;
}
}
- public void featuresAdded()
+ /**
+ * @return a simple list of feature group names or null
+ */
+ public String[] getGroups()
{
- findAllFeatures();
+ buildGroupHash();
+ if (featureGroups != null)
+ {
+ String[] gps = new String[featureGroups.size()];
+ Enumeration gn = featureGroups.keys();
+ int i = 0;
+ while (gn.hasMoreElements())
+ {
+ gps[i++] = (String) gn.nextElement();
+ }
+ return gps;
+ }
+ return null;
+ }
+
+ /**
+ * get visible or invisible groups
+ *
+ * @param visible
+ * true to return visible groups, false to return hidden ones.
+ * @return list of groups
+ */
+ public String[] getGroups(boolean visible)
+ {
+ buildGroupHash();
+ if (featureGroups != null)
+ {
+ Vector gp = new Vector();
+
+ Enumeration gn = featureGroups.keys();
+ while (gn.hasMoreElements())
+ {
+ String nm = (String) gn.nextElement();
+ Boolean state = (Boolean) featureGroups.get(nm);
+ if (state.booleanValue() == visible)
+ {
+ gp.addElement(nm);
+ }
+ }
+ String[] gps = new String[gp.size()];
+ gp.copyInto(gps);
+
+ int i = 0;
+ while (gn.hasMoreElements())
+ {
+ gps[i++] = (String) gn.nextElement();
+ }
+ return gps;
+ }
+ return null;
+ }
+
+ /**
+ * set all feature groups in toset to be visible or invisible
+ *
+ * @param toset
+ * group names
+ * @param visible
+ * the state of the named groups to set
+ */
+ public void setGroupState(String[] toset, boolean visible)
+ {
+ buildGroupHash();
+ if (toset != null && toset.length > 0 && featureGroups != null)
+ {
+ boolean rdrw = false;
+ for (int i = 0; i < toset.length; i++)
+ {
+ Object st = featureGroups.get(toset[i]);
+ if (st != null)
+ {
+ featureGroups.put(toset[i], new Boolean(visible));
+ rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
+ }
+ }
+ if (rdrw)
+ {
+ if (this.av != null)
+ if (this.av.featureSettings != null)
+ {
+ av.featureSettings.rebuildGroups();
+ this.av.featureSettings.resetTable(true);
+ }
+ else
+ {
+ buildFeatureHash();
+ }
+ if (av != null)
+ {
+ av.alignmentChanged(null);
+ }
+ }
+ }
+ }
+
+ /**
+ * analyse alignment for groups and hash tables (used to be embedded in
+ * FeatureSettings.setTableData)
+ *
+ * @return true if features are on the alignment
+ */
+ public boolean buildGroupHash()
+ {
+ boolean alignmentHasFeatures = false;
+ if (featureGroups == null)
+ {
+ featureGroups = new Hashtable();
+ }
+ Vector allFeatures = new Vector();
+ Vector allGroups = new Vector();
+ SequenceFeature[] tmpfeatures;
+ String group;
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ {
+ continue;
+ }
+
+ alignmentHasFeatures = true;
+
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ int index = 0;
+ while (index < tmpfeatures.length)
+ {
+ if (tmpfeatures[index].getFeatureGroup() != null)
+ {
+ group = tmpfeatures[index].featureGroup;
+ if (!allGroups.contains(group))
+ {
+ allGroups.addElement(group);
+
+ boolean visible = true;
+ if (featureGroups.containsKey(group))
+ {
+ visible = ((Boolean) featureGroups.get(group)).booleanValue();
+ }
+ else
+ {
+ featureGroups.put(group, new Boolean(visible));
+ }
+ }
+ }
+
+ if (!allFeatures.contains(tmpfeatures[index].getType()))
+ {
+ allFeatures.addElement(tmpfeatures[index].getType());
+ }
+ index++;
+ }
+ }
+
+ return alignmentHasFeatures;
+ }
+
+ /**
+ * rebuild the featuresDisplayed and renderorder list based on the
+ * featureGroups hash and any existing display state and force a repaint if
+ * necessary
+ *
+ * @return true if alignment has visible features
+ */
+ public boolean buildFeatureHash()
+ {
+ boolean alignmentHasFeatures = false;
+ if (featureGroups == null)
+ {
+ alignmentHasFeatures = buildGroupHash();
+ }
+ if (!alignmentHasFeatures)
+ return false;
+ Hashtable fdisp = av.featuresDisplayed;
+ Vector allFeatures = new Vector();
+ SequenceFeature[] tmpfeatures;
+ String group;
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ {
+ continue;
+ }
+
+ alignmentHasFeatures = true;
+
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ int index = 0;
+ while (index < tmpfeatures.length)
+ {
+ boolean visible = true;
+ if (tmpfeatures[index].getFeatureGroup() != null)
+ {
+ group = tmpfeatures[index].featureGroup;
+ if (featureGroups.containsKey(group))
+ {
+ visible = ((Boolean) featureGroups.get(group)).booleanValue();
+ }
+ }
+
+ if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
+ {
+ allFeatures.addElement(tmpfeatures[index].getType());
+ }
+ index++;
+ }
+ }
+ if (allFeatures.size() > 0)
+ {
+ String[] neworder = new String[allFeatures.size()];
+ int p = neworder.length - 1;
+ for (int i = renderOrder.length - 1; i >= 0; i--)
+ {
+ if (allFeatures.contains(renderOrder[i]))
+ {
+ neworder[p--] = renderOrder[i];
+ allFeatures.removeElement(renderOrder[i]);
+ }
+ else
+ {
+ av.featuresDisplayed.remove(renderOrder[i]);
+ }
+ }
+ for (int i = allFeatures.size() - 1; i > 0; i++)
+ {
+ Object e = allFeatures.elementAt(i);
+ if (e != null)
+ {
+ neworder[p--] = (String) e;
+ av.featuresDisplayed.put(e, getColour((String) e));
+ }
+ }
+ renderOrder = neworder;
+ return true;
+ }
+
+ return alignmentHasFeatures;
+ }
+
+ /**
+ *
+ * @return the displayed feature type as an array of strings
+ */
+ protected String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ synchronized (renderOrder)
+ {
+ typ = new String[renderOrder.length];
+ System.arraycopy(renderOrder, 0, typ, 0, typ.length);
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (av.featuresDisplayed.get(typ[i]) == null)
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ return typ;
}
}
{
void setTransparency(Graphics g, float value)
{
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, value));
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ value));
}
}
git://source.jalview.org / jalview.git / blobdiff